Replace non-linear model with a linear dummy model (working).

gierer-meinhardt/fenics/gierer-meinhardt.py

@@ -30,9 +30,10 @@ def inside(self, x, on_boundary):
 
 # from https://github.com/sebapersson/Master_thesis/blob/1643193a8f786674ce0573518162c0497306935d/Code/Python/RD_models/Run_RD_simulations.py#L21
 a = Constant(0.5)
-b = Constant(2.0)
-gamma = Constant(20)
-d = Constant(50)
+b = Constant(1.0)
+gamma = Constant(0.4)
+d = Constant(0.001)
+e = Constant(0.001)
 
 mesh = UnitSquareMesh(10, 10)
 
@@ -50,7 +51,11 @@ def inside(self, x, on_boundary):
 
 v = TestFunction(V)
 u_n = Function(V)
-u_ini = Expression("x[0]*x[1]", degree=1)
+if args.activator:
+    u_ini = Expression("x[0] * x[1]", degree=1)
+    g = Expression("x[0] * x[0] * x[0]", degree=1)
+elif args.inhibitor:
+    u_ini = Expression("10*(1-x[0])*(1-x[0]) * (1-x[1])*(1-x[1])", degree=1)
 u_n = interpolate(u_ini, V)
 
 dt = precice.initialize(AllDomain(), read_function_space=V, write_object=u_n)
@@ -63,10 +68,9 @@ def inside(self, x, on_boundary):
 
 # from https://github.com/sebapersson/Master_thesis/blob/1643193a8f786674ce0573518162c0497306935d/Code/Python/RD_models/Simulate_RD_models.py#L342-L355
 if args.activator:
-    F = dt_inv*(u - u_n)*v*dx - gamma*(a - b * u + u / f) * v *dx + inner(grad(u), grad(v))*dx
-    #F = dt_inv*(u - u_n)*v*dx - gamma*(a - b * u + u**2 / f) * v *dx + inner(grad(u), grad(v))*dx
+    F = - dt_inv * (u - u_n)*v*dx - f*v*dx - 10e-7 * inner(grad(u), grad(v))*dx + g * v * dx
 elif args.inhibitor:
-    F = dt_inv*(u - u_n)*v*dx - gamma*(f**2 - u)*v*dx + d*inner(grad(u), grad(v))*dx
+    F = - dt_inv * (u - u_n)*v*dx + 10 * f*v*dx - 10e-5 * inner(grad(u), grad(v))*dx
 
 # Time-stepping
 u_np1 = Function(V)

gierer-meinhardt/precice-config.xml

@@ -41,7 +41,7 @@
 
     <coupling-scheme:serial-implicit>
       <participants first="Activator" second="Inhibitor"/>
-      <max-time value="1.0"/>
+      <max-time value="10.0"/>
       <time-window-size value="0.1"/>
       <max-iterations value="100"/>
       <exchange data="Substance" mesh="Activator-Mesh" from="Activator" to="Inhibitor" />